Sisko meets Ezri, the new host of the Dax symbiont, before departing Earth for the planet Tyree with his father, Joseph, and son Jake. Ezri wishes to accompany them on their search for Bajor's mythical Orb of the Emissary, which Sisko has been led to believe exists. Back at the station, Kira prepares a blockade to stop the Romulans, who have placed weapons on a Bajoran moon. On a Klingon ship, Worf, O'Brien, Bashir, and Quark embark on a mission of their own: to destroy a Dominion shipyard, thus securing a place for the spirit of Worf's dead wife Jadzia in the sacred Klingon afterlife of Sto-vo-kor.
Sisko and his crew arrive on Tyree. Guided by his visions, they begin a long trek across the vast desert terrain. Eventually, Sisko stops and digs on a seeming whim, while his father, son, and Ezri can only watch.
Kira sets her blockade with old Bajoran ships, and four Romulan warbirds approach, just hours away; while Worf and his companions prepare to face their own danger in Jadzia's name. On Tyree, Sisko's digging uncovers an Orb ark, but dangerous visions cause him to hesitate from exposing the Orb within.
Back on the Klingon ship, Worf, having reached the star system where the shipyard is located, masterminds a plan in which his vessel will fly toward the sun and trigger a plasma ejection that will destroy the Dominion facility and illuminate the gates of Sto-vo-kor for Jadzia. Meanwhile, Sisko's visions force him to inexplicably and hastily bury the ark containing the Orb without opening it.
Worf and his comrades manage to execute their plan and demolish the shipyard — a victory that finally allows for Jadzia's entrance into Sto-vo-kor. At the same time, Kira successfully causes the Romulans to back down. On Tyree, Ezri forces Sisko to open the ark. But when he does, an energy vortex is unleashed which opens the wormhole and expels from it the Pah-wraiths — the enemies of the Prophets — who sealed the anomaly. His mission successful, Sisko encounters what appears to be his dead mother Sarah. After commending him, she reveals that she is one of the wormhole aliens, who took over the real Sarah's body years ago to ensure Sisko's birth and the fulfillment of his destiny.